subject:"Re\: \[gmx\-users\] Mass and charge data are missing in \[ atomtypes \] section."

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-13 Thread Dd H

Thank you so much!

On 13 October 2016 at 20:07, Justin Lemkul  wrote:

>
>
> On 10/12/16 11:06 PM, Dd H wrote:
>
>> I found these words in the GROMACS v4.5.5 manual:
>>
>> *[ atoms ] : defines the molecule, where nr and type are fixed, the rest
>> is
>> user defined. So*
>> *atom can be named as you like, cgnr made larger or smaller (if possible,
>> the total charge of a **charge group should be zero), and charges can be
>> changed here too.*
>>
>> So does it means the mass and charge of [ atomtypes ] section could be
>> modified in [ atoms ] section?
>>
>>
> Look at the example in section 5.7.2.  Note that masses are absent.  If
> masses are not provided in [atoms], they are referenced from [atomtypes].
> Charges present in [atomtypes] are never used for anything and must be
> specified in [atoms].
>
> -Justin
>
>
> On 12 October 2016 at 23:30, Alan  wrote:
>>
>> But read the GMX manual to understand why it's all fine.
>>>
>>> On 12 October 2016 at 13:29, Dd H  wrote:
>>>
>>> Thank you!

 On 12 October 2016 at 19:50, Alan  wrote:

 It's all fine.
>
> On 12 October 2016 at 12:34, Dd H  wrote:
>
> I use this command:
>> acpype -p filename.prmtop -x filename.inpcrd
>>
>> It generates parameter files for GROMACS and my question is about the
>>
> .top
>
>> file of outputs.
>>
>> On 12 October 2016 at 18:22, Alan  wrote:
>>
>> Which acpype command did you specifically used?
>>>
>>> acpype may be able to use Antechamber and calculate partial
>>>
>> charges.
>>>
 See
>
>> acpype -h
>>>
>>> On 12 October 2016 at 09:56, Dd H  wrote:
>>>
>>> Hi everyone,
 I generated a .top file of a ligand using acpype for MD

>>> simulations.

> There
>>>
 are some new atom types in [ atomtypes ] section, but the data of

>>> mass
>
>> and
>>>
 charge columns of the section are zeros. However they can be

>>> found
>>>
 in

> the [
>>>
 atoms ] section. Can you tell me if this file is ok for MD

>>> simulations?
>
>> Thank you in advance!

 Dading Huang
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 or
>
>> send a mail to gmx-users-requ...@gromacs.org.


>>>
>>>
>>> --
>>> Alan Wilter SOUSA da SILVA, DSc
>>> Senior Bioinformatician, UniProt
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>> Tel: +44 (0)1223 494588
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>> or

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>>>
>>> --
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>>
> or
>>>
 send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
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>
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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-13 Thread Justin Lemkul




On 10/12/16 11:06 PM, Dd H wrote:

I found these words in the GROMACS v4.5.5 manual:

*[ atoms ] : defines the molecule, where nr and type are fixed, the rest is
user defined. So*
*atom can be named as you like, cgnr made larger or smaller (if possible,
the total charge of a **charge group should be zero), and charges can be
changed here too.*

So does it means the mass and charge of [ atomtypes ] section could be
modified in [ atoms ] section?



Look at the example in section 5.7.2.  Note that masses are absent.  If masses 
are not provided in [atoms], they are referenced from [atomtypes].  Charges 
present in [atomtypes] are never used for anything and must be specified in [atoms].


-Justin


On 12 October 2016 at 23:30, Alan  wrote:


But read the GMX manual to understand why it's all fine.

On 12 October 2016 at 13:29, Dd H  wrote:


Thank you!

On 12 October 2016 at 19:50, Alan  wrote:


It's all fine.

On 12 October 2016 at 12:34, Dd H  wrote:


I use this command:
acpype -p filename.prmtop -x filename.inpcrd

It generates parameter files for GROMACS and my question is about the

.top

file of outputs.

On 12 October 2016 at 18:22, Alan  wrote:


Which acpype command did you specifically used?

acpype may be able to use Antechamber and calculate partial

charges.

See

acpype -h

On 12 October 2016 at 09:56, Dd H  wrote:


Hi everyone,
I generated a .top file of a ligand using acpype for MD

simulations.

There

are some new atom types in [ atomtypes ] section, but the data of

mass

and

charge columns of the section are zeros. However they can be

found

in

the [

atoms ] section. Can you tell me if this file is ok for MD

simulations?

Thank you in advance!

Dading Huang
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gmx-users

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send a mail to gmx-users-requ...@gromacs.org.





--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Dd H

I found these words in the GROMACS v4.5.5 manual:

*[ atoms ] : defines the molecule, where nr and type are fixed, the rest is
user defined. So*
*atom can be named as you like, cgnr made larger or smaller (if possible,
the total charge of a **charge group should be zero), and charges can be
changed here too.*

So does it means the mass and charge of [ atomtypes ] section could be
modified in [ atoms ] section?

On 12 October 2016 at 23:30, Alan  wrote:

> But read the GMX manual to understand why it's all fine.
>
> On 12 October 2016 at 13:29, Dd H  wrote:
>
> > Thank you!
> >
> > On 12 October 2016 at 19:50, Alan  wrote:
> >
> > > It's all fine.
> > >
> > > On 12 October 2016 at 12:34, Dd H  wrote:
> > >
> > > > I use this command:
> > > > acpype -p filename.prmtop -x filename.inpcrd
> > > >
> > > > It generates parameter files for GROMACS and my question is about the
> > > .top
> > > > file of outputs.
> > > >
> > > > On 12 October 2016 at 18:22, Alan  wrote:
> > > >
> > > > > Which acpype command did you specifically used?
> > > > >
> > > > > acpype may be able to use Antechamber and calculate partial
> charges.
> > > See
> > > > > acpype -h
> > > > >
> > > > > On 12 October 2016 at 09:56, Dd H  wrote:
> > > > >
> > > > > > Hi everyone,
> > > > > > I generated a .top file of a ligand using acpype for MD
> > simulations.
> > > > > There
> > > > > > are some new atom types in [ atomtypes ] section, but the data of
> > > mass
> > > > > and
> > > > > > charge columns of the section are zeros. However they can be
> found
> > in
> > > > > the [
> > > > > > atoms ] section. Can you tell me if this file is ok for MD
> > > simulations?
> > > > > > Thank you in advance!
> > > > > >
> > > > > > Dading Huang
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Alan Wilter SOUSA da SILVA, DSc
> > > > > Senior Bioinformatician, UniProt
> > > > > European Bioinformatics Institute (EMBL-EBI)
> > > > > European Molecular Biology Laboratory
> > > > > Wellcome Trust Genome Campus
> > > > > Hinxton
> > > > > Cambridge CB10 1SD
> > > > > United Kingdom
> > > > > Tel: +44 (0)1223 494588
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > >
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> > > >
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Senior Bioinformatician, UniProt
> > > European Bioinformatics Institute (EMBL-EBI)
> > > European Molecular Biology Laboratory
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > United Kingdom
> > > Tel: +44 (0)1223 494588
> > > --
> > > Gromacs Users mailing list
> > >
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> > >
> > --
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> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Alan

But read the GMX manual to understand why it's all fine.

On 12 October 2016 at 13:29, Dd H  wrote:

> Thank you!
>
> On 12 October 2016 at 19:50, Alan  wrote:
>
> > It's all fine.
> >
> > On 12 October 2016 at 12:34, Dd H  wrote:
> >
> > > I use this command:
> > > acpype -p filename.prmtop -x filename.inpcrd
> > >
> > > It generates parameter files for GROMACS and my question is about the
> > .top
> > > file of outputs.
> > >
> > > On 12 October 2016 at 18:22, Alan  wrote:
> > >
> > > > Which acpype command did you specifically used?
> > > >
> > > > acpype may be able to use Antechamber and calculate partial charges.
> > See
> > > > acpype -h
> > > >
> > > > On 12 October 2016 at 09:56, Dd H  wrote:
> > > >
> > > > > Hi everyone,
> > > > > I generated a .top file of a ligand using acpype for MD
> simulations.
> > > > There
> > > > > are some new atom types in [ atomtypes ] section, but the data of
> > mass
> > > > and
> > > > > charge columns of the section are zeros. However they can be found
> in
> > > > the [
> > > > > atoms ] section. Can you tell me if this file is ok for MD
> > simulations?
> > > > > Thank you in advance!
> > > > >
> > > > > Dading Huang
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Alan Wilter SOUSA da SILVA, DSc
> > > > Senior Bioinformatician, UniProt
> > > > European Bioinformatics Institute (EMBL-EBI)
> > > > European Molecular Biology Laboratory
> > > > Wellcome Trust Genome Campus
> > > > Hinxton
> > > > Cambridge CB10 1SD
> > > > United Kingdom
> > > > Tel: +44 (0)1223 494588
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
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> or
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> > > >
> > > --
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> > >
> >
> >
> >
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > Senior Bioinformatician, UniProt
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > United Kingdom
> > Tel: +44 (0)1223 494588
> > --
> > Gromacs Users mailing list
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
-- 
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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Dd H

Thank you!

On 12 October 2016 at 19:50, Alan  wrote:

> It's all fine.
>
> On 12 October 2016 at 12:34, Dd H  wrote:
>
> > I use this command:
> > acpype -p filename.prmtop -x filename.inpcrd
> >
> > It generates parameter files for GROMACS and my question is about the
> .top
> > file of outputs.
> >
> > On 12 October 2016 at 18:22, Alan  wrote:
> >
> > > Which acpype command did you specifically used?
> > >
> > > acpype may be able to use Antechamber and calculate partial charges.
> See
> > > acpype -h
> > >
> > > On 12 October 2016 at 09:56, Dd H  wrote:
> > >
> > > > Hi everyone,
> > > > I generated a .top file of a ligand using acpype for MD simulations.
> > > There
> > > > are some new atom types in [ atomtypes ] section, but the data of
> mass
> > > and
> > > > charge columns of the section are zeros. However they can be found in
> > > the [
> > > > atoms ] section. Can you tell me if this file is ok for MD
> simulations?
> > > > Thank you in advance!
> > > >
> > > > Dading Huang
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Senior Bioinformatician, UniProt
> > > European Bioinformatics Institute (EMBL-EBI)
> > > European Molecular Biology Laboratory
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > United Kingdom
> > > Tel: +44 (0)1223 494588
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
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> Cambridge CB10 1SD
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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Alan

It's all fine.

On 12 October 2016 at 12:34, Dd H  wrote:

> I use this command:
> acpype -p filename.prmtop -x filename.inpcrd
>
> It generates parameter files for GROMACS and my question is about the .top
> file of outputs.
>
> On 12 October 2016 at 18:22, Alan  wrote:
>
> > Which acpype command did you specifically used?
> >
> > acpype may be able to use Antechamber and calculate partial charges. See
> > acpype -h
> >
> > On 12 October 2016 at 09:56, Dd H  wrote:
> >
> > > Hi everyone,
> > > I generated a .top file of a ligand using acpype for MD simulations.
> > There
> > > are some new atom types in [ atomtypes ] section, but the data of mass
> > and
> > > charge columns of the section are zeros. However they can be found in
> > the [
> > > atoms ] section. Can you tell me if this file is ok for MD simulations?
> > > Thank you in advance!
> > >
> > > Dading Huang
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > Senior Bioinformatician, UniProt
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > United Kingdom
> > Tel: +44 (0)1223 494588
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Dd H

I use this command:
acpype -p filename.prmtop -x filename.inpcrd

It generates parameter files for GROMACS and my question is about the .top
file of outputs.

On 12 October 2016 at 18:22, Alan  wrote:

> Which acpype command did you specifically used?
>
> acpype may be able to use Antechamber and calculate partial charges. See
> acpype -h
>
> On 12 October 2016 at 09:56, Dd H  wrote:
>
> > Hi everyone,
> > I generated a .top file of a ligand using acpype for MD simulations.
> There
> > are some new atom types in [ atomtypes ] section, but the data of mass
> and
> > charge columns of the section are zeros. However they can be found in
> the [
> > atoms ] section. Can you tell me if this file is ok for MD simulations?
> > Thank you in advance!
> >
> > Dading Huang
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

2016-10-12 Thread Alan

Which acpype command did you specifically used?

acpype may be able to use Antechamber and calculate partial charges. See
acpype -h

On 12 October 2016 at 09:56, Dd H  wrote:

> Hi everyone,
> I generated a .top file of a ligand using acpype for MD simulations. There
> are some new atom types in [ atomtypes ] section, but the data of mass and
> charge columns of the section are zeros. However they can be found in the [
> atoms ] section. Can you tell me if this file is ok for MD simulations?
> Thank you in advance!
>
> Dading Huang
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

Re: [gmx-users] Mass and charge data are missing in [ atomtypes ] section.

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